After consulting with his assistant, referee Mark Clattenburg ruled that Luke Shaw pushed Grant Holt just inside the penalty area in the Barclays Premier League match between the two sides on .
Holt missed the subsequent spot-kick with Artur Boruc keeping out his effort, but Southampton players continued to protest after the final whistle, and were joined on the pitch by manager Mauricio Pochettino.
The club has until 4pm on Friday to respond to the charge.
Crystal Palace winger Wilfried Zaha and manager Ian Holloway have also been charged following Saturday's clash with Leeds.
Zaha has been charged with improper conduct after appearing to make an offensive gesture towards the Leeds fans.
The 20-year-old, who in January agreed a move to Leeds' historic rivals Manchester United, later apologised for his actions on Twitter.
He wrote: "I...wanted to apologise for the gesture I did towards the Leeds fans in yesterday's [Saturday] game. Very unprofessional from me."
Holloway, who was angry at some of the refereeing decisions during the 2-2 draw, has been charged for alleged misconduct towards the match officials.
Both Zaha and Holloway have until 4pm on Friday to respond to the charges.